Friday, June 29, 2012

Current adaptation research is increasingly employing genome scans to search for signatures of selection in the form of markers displaying relatively elevated divergence (typically quantified by Fst) between populations in ecologically distinct habitats. While performing such a study using RADseq in threespine stickleback (see Roesti et al. 2012, Mol. Ecol.), we came across an analytical issue crucial to genome scans, but largely ignored so far.

The point is that polymorphisms with a low minor allele frequency (MAF) are not informative in inferring genetic differentiation between populations and can thus bias the outcome and interpretation of genome scans. Such low-MAF polymorphisms obviously arise easily from technical problems (e.g. sequencing or PCR errors), but theory predicts clearly that a high frequency of low-MAF polymorphisms (especially singletons) is a natural feature of biological samples. No matter how low-MAF polymorphisms arise, we argue in our just-published BMC Evolutionary Biology paper (Roesti et al. 2012, in press) that genetic markers with a low MAF can bias any study – not only genome scans – that involves Fst calculation or any other divergence metric.

The reason why low-MAF markers should be discarded is that researchers conducting genome scans make the tacit assumption that genetic markers adequately capture two key processes – hitchhiking with a selected locus, and drift. The markers used for a genome scan thus need to adequately mirror these historical processes. However, this is not the case for low-MAF polymorphisms because they mostly represent short-lived mutations without historical depth, and their highly imbalanced allele frequencies prevent them from displaying the genetic footprints of selective sweeps. In other words, genetic markers with a low MAF simply lack the potential to capture possible frequency shifts at close-by genomic regions. The best way to think about this is to toy around with this idea even further: if a monomorphic locus was included in a genome scan study, there would be a clear bias in the outcome because this locus obviously cannot capture hitchhiking and drift even if these processes occur! For exactly that reason, nobody thinks about using monomorphic loci for genome scans, but it is generally overlooked that low-MAF markers are nearly as uninformative as fully monomorphic loci.

Again, low-MAF polymorphisms are predicted to be very common in any study system. Marker numbers reported in genome scans studies that do not exclude uninformative polymorphisms are thus likely massively inflated, and divergence patterns and outliers potentially inaccurate. For instance, in our recent genome scans, we applied a minimum threshold of 25% for the minor allele. This leads to a marker loss of 60-70%. However, the remaining markers were really informative. In the BMC paper we make suggestions how this problem can be addressed.

Overall, our study highlights the major need to carefully handle and interpret molecular data, especially in the current golden age of evolutionary genetics and genomics.

Sunday, June 24, 2012

Evolution 2012 is coming to Ottawa! It promises to be utter mayhem — up to 18 parallel sessions at any given time. The Hendry Lab will be there in force; to help you watch every one of our talks (you know you want to!) here they are, assembled in one place:

I think that might be just about it. Sheesh. Times/rooms are subject to change, of course, so check the schedule to avoid getting tears in your beer later. And if you're giving a talk at the conference related to eco-evolutionary dynamics, post it in the comments! See you in Ottawa!

Thursday, June 21, 2012

I recently helped Marianne Elias, Rui Faria, and Zach Gompert to edit a special issue on the topic of Ecological Speciation for the International Journal of Ecology. The special issue is now online and is entirely free to download. The issue includes19 papers from many of the leading authors in ecological speciation.

Saturday, June 9, 2012

(I am posting a press release from McGill related to a paper that has just officially come out.)

A current controversy raging in evolutionary biology is whether adaptation to new environments is the result of many genes, each of relatively small effect, or just a few genes of large effect. A new study published in Molecular Ecology strongly supports the first "many-small" hypothesis. McGill University professor Andrew Hendry, from the Department of Biology and the Redpath Museum, and evolutionary geneticists at Basel University in Switzerland, studied how threespine stickleback fish adapted to lake and stream environments in British Columbia, Canada.

The authors used cutting-edge genomic methods to test for genetic differences at thousands of positions ("loci") scattered across the stickleback genome. Very large genetic differences between lake and stream stickleback were discovered at more than a dozen of these loci, which is considerably more than expected under the alternative "few-large" hypothesis.

By examining four independently evolved lake-stream population pairs, the researchers were further able to show that increasing divergence between the populations involved genetic differences that were larger and present at more and more loci.

As these results were obtained using new high-resolution genetic methods, it is conceivable that previous perceptions of adaptation as being a genetically simple process are simply the result of a bias resulting from previous lower-resolution genomic methods.

"I suspect that as more and more studies use these methods, the tide of opinion will swerve strongly to the view that adaptation is a complex process that involves many genes spread across diverse places in the genome," says Prof. Hendry.

PZ has chosen an Icelandic theme for this month. I don't have any photos from Iceland, since I've never been there myself; but here's a photo I took in Yellowstone National Park, which is kind of a mini-Iceland in the middle of the U.S.:

Photo credit: Ben Haller, 2009.

Late-breaking news: my parents were recently in Iceland, so here's a photo they took of Arctic terns in a stiff wind, against a panoramic Icelandic backdrop near Snaefellsness. No doubt, it being Iceland, the whole scene is about to be engulfed by floods of molten lava.

Tuesday, June 5, 2012

If you are going to have your research filmed, you might as
well go the whole hog: high definition 3D shown in an IMAX theater with Sir
David Attenborough narrating. In theory, that is what will happen with Team
Pinzones, our hard working and long suffering research team studying the
evolution of Darwin’s finches (pinzones). This week I was back in Galapagos with team
member Jaime Chaves to recreate our fascinating and exciting procedure for the
cameras: setting nets, catching birds, putting on bands, measuring wings,
measuring legs, measuring beaks,
measuring heads, photographing, weighing, and releasing (no blood samples this
time). It was quite an adventure.

Team Pinzones goes before the (3D) camera. (Photo by Aspen Hendry.)

First, the permits weren’t approved until the very last
minute – after the last minute actually. Not only did the film crew (Colossus
Productions filming for BBC) need permits to film our work but we also needed
permits to speak to them about our work. That achieved the day after we arrived,
filming was set to occur in a few days. The next problem, however, was that the
filming equipment was delayed – 5 tons of it! Customs in Guayaquil had taken
every single part of the equipment and removed it from the packaging and
photographed it. This delayed things for a few days but then the equipment was
finally shipped – except the batteries, which were deemed hazardous cargo. This
battery delay pushed us past the official filming date, and so we had to
change our flights by two more days. Having done so, the batteries arrived the
next day but one piece was still missing – the base for the crane. Yes, the
crane. They needed a crane to film our work. So it came down to one final day
for filming before we really needed to leave Galapagos. Would the crane base
come in time?﻿﻿﻿﻿

It's not your mother's camera. (Photo by Jaime Chaves.)

Indeed it did, just in time for filming on that last day. The next worry – for us at least – was that
the 3D camera, the crane, and all the other equipment would be so heavy and cumbersome and finnicky that the whole
procedure would be very slow. It takes a long time to move the stuff around and they
wanted to film several locations along the El Garrapatero beach – itself a
decent walk from the parking lot. The equipment was all ferried down the day
before and then we all arrived at first light on the filming day. But would
there be enough time to film all the bird sequences before it got too hot for the birds –
normally about 10 am? The answer normally would be an emphatic no because it
generally gets really sunny and baking around that time. But fortune smiled
upon us beyond all expectation and it was cloudy and windy all day. The next
concern was whether we could catch enough birds at the right times? Sometimes
at El Garrapatero, we can go a long time without catching birds and that
might be a problem since we didn’t want to hold any individual bird for too
long. We started with one net and, within half an hour, we had a male and
female fuliginosa (small ground finch), a male and female fortis (medium ground
finch), and a female scandens (cactus finch) – each of the species we might
reasonably expect to catch here. Let’s start filming.

Getting a finch ready for its close-up. (Photo by Jaime Chaves.)

First we did the close-ups with the huge camera nestled
right up next to our hands (I had to bend my neck around the camera to see what I was measuring).
At the end of this close-up period, we suggested it would be good to film the
large and small beaked morphs of the fortis – the phenomenon we study at this
site – but we didn’t have a small morph bird already captured. So we started
filming a medium bird alongside a very large one but, as I was holding the
birds for the camera, Jaime ran off to see if he could set the net again and
catch a smaller bird. Five minutes later he was back with the perfect bird. After
that minor miracle the crew needed wider angle shots of the same thing but most of the
birds had been held in their bags for an hour already and they should be set free. So we went back
to the net, set it again, and had 5 birds of all three species in half an hour.
It was almost like we could just “dial a finch” and place our order, having it
delivered at a pace that would shame pizza delivery.

Even the banding equipment gets a close-up.

Then it was time for even wider shots – and now the crane
would be called into action. We were to walk from the net with birds in their
bags to our banding station and the 3D camera would swoop around us presumably
giving everyone vertigo in the theater. So we did this a few times for
practice and then did the actual sequence. As we sat down on this first take and
started to process the birds, we noticed that there were 4 or 5 finches hopping around not 2 meters from where we were processing. “Hey you guys
should film those birds,” we said. Yeah right. What are the chances that they
could set this complicated camera up on a huge crane, have some birds hop down
at random at just the perfect distance, swoop the camera on the crane 180
degrees, and have it plop down in front of the finches without them leaving. Well,
not only did that happen but as soon as the camera came near to the birds a bunch more
arrived until nine of them were all hopping around right in front of the
camera. They filmed this for a minute and then swooped around to show us
processing finches right beside the free-flying finches in one continuous sequence. Dial a finch
indeed.

Moments before the finches arrived.

Next it was time to film us taking a bird from the net. As
we did this, the entire crane was moved about 40 meters to a rock promontory between
two patches of sandy beach and reconstituted on a wooden platform that had been
constructed just that day as the other filming was going on. This platform was quite
substantial because it also had a rail on it so that the entire crane could be
rolled along smoothly as it swooped around a cactus and could then be pulled
back to show us walking across the beach and then the lava toward our net. We
got to watch them practice their crane moves with one "grip" holding the
counterweight at one end and swooping it around and the other grip rolling the
entire apparatus along the rail. Then we had to go off and perform our walk for
the real filming. After that, with the light just petering out, it was time for
an interview at yet another location – sitting on some (reasonably comfortable)
lava beside the beach. Then 5 tons had to be carried back up to the parking
lot. It was a good thing 24 people were involved.

The camera on the crane on the rails on the platform.

This experience taught me several things. First, 3D is much
much much more complicated than 2D – the camera is huge and needs to be
calibrated before every shot. Second, those shots you see in BBC videos require
an immense amount of work – and now I know what a “grip” really does, although
I forgot to ask what made one of the grips the “best boy grip” that you often see acknowledged in film credits. Third, film makers may often be
unlucky with the elements or animals – as you so often see in the behind-the-scenes
stuff for BBC videos – but the opposite can also be true. The weather we had
was perfect – beyond perfect. It was literally the best possible weather for
working with birds ALL DAY LONG. And the birds were incredibly accommodating.
With a single net we could catch exactly what we wanted within 15 minutes at
any time of the day, which is definitely not typical. And then a whole gaggle
of finches shows up right in the perfect place for the camera already on a
crane. I am pretty sure the film makers don’t realize how incredibly lucky we
all were. And maybe those extra birds we captured and measured will be the ones
that make all our statistical tests significant.

Now we just have to wait a
year or so to see how it looks in IMAX 3D with narration by you know who (of course, our stuff will be only a tiny fraction of the entire movie). In the meantime, we need to interest someone in Team Stickleback IMAX 3D and Team Guppy IMAX 3D.

Note: Special thanks to key recent Team Pinzones members Jeff Podos, Luis Fernando De Leon, and Joost Raeymaekers.

Monday, June 4, 2012

Today, our blog joins the Black Out Speak Out movement to protest the Canadian government's Bill C-38 which would severely cripple many of Canada's important environmental laws. For more information about what the bill will do, more information is here.